Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values

• Published in: Bioinformatics Vol. 28; no. 22; pp. 2986 - 2988
• Main Authors: PEDERSEN, Brent S, SCHWARTZ, David A, YANG, Ivana V, KECHRIS, Katerina J
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.11.2012
• Subjects: Applications Note; Assessments; Autocorrelation; Binding; Biological and medical sciences; Computer programs; DNA Probes - analysis; DNA Probes - genetics; Enrichment; Fundamental and applied biological sciences. Psychology; General aspects; Genome-Wide Association Study; Genomics - methods; Humans; Libraries; Licenses; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Programming Languages; Sequence Analysis, DNA; Software; Grouping; Software
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/bts545

comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions. In addition, tools are provided for visualization and assessment. We provide validation and example uses on bisulfite-seq with P-values from Fisher's exact test, tiled methylation probes using a linear model and Dam-ID for chromatin binding using moderated t-statistics. Because the library accepts input in a simple, standardized format and is unaffected by the origin of the P-values, it can be used for a wide variety of applications. comb-p is maintained under the BSD license. The documentation and implementation are available at https://github.com/brentp/combined-pvalues. bpederse@gmail.com